From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Dec 03 2013 - 01:55:14 CST
Hello:
Bug in T-REMD with colvars could hopefully simply mean bug in information
about T-REMD with colvars.
Some time ago I asked - on general grounds - advice on how to manage to get
colvars state be recognized by restarted replicas. I got no answer. Here, I
am more specific on this issue, working with namd2.10, although same issue
with namd2.9.
Setting in namd config file (alanin_based.namd in the alanin t-remd example
provided by namd)
# constraints
colvars on ; # provide colvarsConfig (and colvarsINput if
restart)
colvarsConfig ./P2i_rmsd-colvars.in
gives correct
fold_P2i.job0.0.colvars.state
fold_P2i.job0.0.colvars.traj
in replica/0, like in all other 31 replicas of my T-REMD. However, what is
not provided anywhere is what the system asks (see below, please) when I
add a line for colvarsInput into file replica.namd as follows:
if {$i_run} { #restart
bincoordinates $restart_root.$replica_id.coor
binvelocities $restart_root.$replica_id.vel
extendedSystem $restart_root.$replica_id.xsc
colvarsInput $restart_root.$replica_id.colvars.state
} else {
temperature $NEWTEMP
}
Thus, the error arises in the .err file:
REPLICA 23 FATAL ERROR: Error in the collective variables module: exiting.
Looking at the replica 23 log file, one learns that:
colvars: Collective variables biases initialized, 1 in
total.fold_P2i.job0.restart500.23.colvars.state
colvars:
----------------------------------------------------------------------
colvars: Error: in opening restart file
"output/23/fold_P2i.job0.restart500.23.colvars.state".
*******************************
In this scenario, I wish that the line "colvarsInput
$restart_root.$replica_id.colvars.state" I added to replica.namd should be
reformulated, or placed elsewhere (in the namd config file?). That
statement was introduced on imitation of umbrella sampling.
I hope now that developers will be so kind to correct my faults or my
overlooking any T-REMD output, if any, to the benefit of all namd users
too. Or provide anyway a solution to carry out correctly T-REMD with
colvars.
Thanks a lot for advice
francesco pietra
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